First test for prepare:filter_genomes

test/test_unit/test_prepare/test_filter.py

@@ -6,5 +6,59 @@ Unit tests for the download_genomes_func submodule in prepare module
 """
 import os
 import logging
+import shutil
 
 import PanACoTA.prepare_module.filter_genomes as filterg
+
+DATA_TEST_DIR = os.path.join("test", "data", "prepare")
+
+def test_write_output(caplog):
+    """
+    Check that the files with kept genomes and discarded genomes are created
+    """
+    corresp_genomes = {"ACOR001": "ACOR001.0519.fna.gz", "ACOR002": "ACOR002.0519.fna.gz",
+                       "ACOR003": "ACOR003.0519.fna.gz"}
+    sorted_genomes = [os.path.join(DATA_TEST_DIR, "genomes", "refseq", "bacteria", gen, gz)
+                      for gen, gz in corresp_genomes.items()]
+    genomes = {genome_file:["gname", "ori_name", "path_annotate", 12, 10, 1]
+               for genome_file in sorted_genomes}
+    genomes["toto"] = ['totoname', 'ori toto', 'path_toto', 13, 5, 6]
+    genomes_removed = {"genome": ["ref", 10]}
+
+    # Define output directory for generated files
+    outdir = os.path.join(DATA_TEST_DIR, "test_filter_write_output")
+    os.makedirs(outdir)
+    gspecies = "Acetobacter_fabarum"
+    min_dist = 0.06
+
+    # Check everything works without error
+    assert filterg.write_outputfiles(genomes, sorted_genomes,
+                                     genomes_removed, outdir, gspecies, min_dist) == 0
+
+    # Check outfiles exist
+    list_file = os.path.join(outdir, "LSTINFO-Acetobacter_fabarum-filtered-0.06.txt")
+    discard_file = os.path.join(outdir, "discarded-by-minhash-Acetobacter_fabarum-0.06.txt")
+    assert os.path.isfile(list_file)
+    assert os.path.isfile(discard_file)
+
+    # Check content of out files
+    with open(list_file) as lf:
+        # Check header
+        assert "to_annotate\tgsize\tnb_conts\tL90" in lf.readline()
+        # Check there are 3 genomes, with expected information
+        assert "path_annotate 12\t10\t1" in lf.readline()
+        assert "path_annotate\t12\t10\t1" in lf.readline()
+        assert "path_annotate\t12\t10\t1" in lf.readline()
+        assert "path_annotate\t12\t10\t1" in lf.readline()
+        assert lf.readline() == "\n"
+
+    with open(discard_file) as df:
+        # Check header
+        assert "genome_name\tproblem_compared_with\tdist" in df.readline()
+        # Check genome line
+        assert "genome" in df.readline()
+        # Check no more genomes
+        assert df.readline() == '\n'
+
+    # Remove test folder
+    # shutil.rmtree(outdir)
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